1
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Fišer Ž, Whitehorn H, Furness T, Trontelj P, Protas M. Genetic bias in repeated evolution of pigment loss in cave populations of the Asellus aquaticus species complex. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38828691 DOI: 10.1002/jez.b.23256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/26/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024]
Abstract
Similar phenotypes can evolve repeatedly under the same evolutionary pressures. A compelling example is the evolution of pigment loss and eye loss in cave-dwelling animals. While specific genomic regions or genes associated with these phenotypes have been identified in model species, it remains uncertain whether a bias towards particular genetic mechanisms exists. An isopod crustacean, Asellus aquaticus, is an ideal model organism to investigate this phenomenon. It inhabits surface freshwaters throughout Europe but has colonized groundwater on multiple independent occasions and evolved several cave populations with distinct ecomorphology. Previous studies have demonstrated that three different cave populations utilized common genetic regions, potentially the same genes, in the evolution of pigment and eye loss. Expanding on this, we conducted analysis on two additional cave populations, distinct either phylogenetically or biogeographically from those previously examined. We generated F2 hybrids from cave × surface crosses and tested phenotype-genotype associations, as well as conducted complementation tests by crossing individuals from different cave populations. Our findings revealed that pigment loss and orange eye pigment in additional cave populations were associated with the same genomic regions as observed in the three previously tested cave populations. Moreover, the lack of complementation across all cross combinations suggests that the same gene likely drives pigment loss. These results substantiate a genetic bias in the recurrent evolution of pigment loss in this model system. Future investigations should focus on the cause behind this bias, possibly arising from allele recruitment from ancestral surface populations' genetic variation or advantageous allele effects via pleiotropy.
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Affiliation(s)
- Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Hana Whitehorn
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Tia Furness
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Meredith Protas
- Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, California, USA
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2
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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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3
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Laine J, Mak SST, Martins NFG, Chen X, Gilbert MTP, Jones FC, Pedersen MW, Romundset A, Foote AD. Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation. Curr Biol 2024; 34:1142-1147.e6. [PMID: 38350445 DOI: 10.1016/j.cub.2024.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms1,2,3 and to thereby potentially provide an understanding of the evolutionary histories of past populations.4,5 To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.6,7 Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies1,2,3 to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)8 were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches9,10,11 and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.
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Affiliation(s)
- Jan Laine
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway
| | - Sarah S T Mak
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Nuno F G Martins
- Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Xihan Chen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Center for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, 1353 Copenhagen, Denmark
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Andrew D Foote
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Erling Skakkes gate 47A, 7012 Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316 Oslo, Norway.
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4
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Meng QL, Qiang CG, Li JL, Geng MF, Ren NN, Cai Z, Wang MX, Jiao ZH, Zhang FM, Song XJ, Ge S. Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara. Mol Ecol 2024; 33:e17268. [PMID: 38230514 DOI: 10.1111/mec.17268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.
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Affiliation(s)
- Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng-Gen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ji-Long Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Hui Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian-Jun Song
- Key Laboratory of Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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5
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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6
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Lloyd E, Privat M, Sumbre G, Duboué ER, Keene AC. A protocol for whole-brain Ca 2+ imaging in Astyanax mexicanus, a model of comparative evolution. STAR Protoc 2023; 4:102517. [PMID: 37742184 PMCID: PMC10520939 DOI: 10.1016/j.xpro.2023.102517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/17/2023] [Accepted: 07/27/2023] [Indexed: 09/26/2023] Open
Abstract
In this protocol, we describe a comparative approach to study the evolution of brain function in the Mexican tetra, Astyanax mexicanus. We developed surface fish and two independent populations of cavefish with pan-neuronal expression of the Ca2+ sensor GCaMP6s. We describe a methodology to prepare samples and image activity across the optic tectum and olfactory bulb.
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Affiliation(s)
- Evan Lloyd
- Department of Biology, Texas A&M University, College Station, TX 77840, USA.
| | - Martin Privat
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - German Sumbre
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Erik R Duboué
- Harriet Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX 77840, USA.
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7
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Ye Z, Pfrender ME, Lynch M. Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates. Genome Biol Evol 2023; 15:evad202. [PMID: 37946625 PMCID: PMC10664402 DOI: 10.1093/gbe/evad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. In this study, we compared population-genomics data between Daphnia pulex and Daphnia pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. Daphnia pulicaria has lower genome-wide nucleotide diversity, a smaller effective population size, a higher incidence of private alleles, and a substantially more linkage disequilibrium than D. pulex. Positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended life span in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Additionally, we found that the two species have similar average evolutionary rates at the DNA-sequence level, although approximately 160 genes have significantly different rates in the two lineages. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.
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Affiliation(s)
- Zhiqiang Ye
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
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8
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Matthews DG, Dial TR, Lauder GV. Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution. Integr Comp Biol 2023; 63:843-859. [PMID: 37422435 DOI: 10.1093/icb/icad096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023] Open
Abstract
To understand the complexities of morphological evolution, we must understand the relationships between genes, morphology, performance, and fitness in complex traits. Genomicists have made tremendous progress in finding the genetic basis of many phenotypes, including a myriad of morphological characters. Similarly, field biologists have greatly advanced our understanding of the relationship between performance and fitness in natural populations. However, the connection from morphology to performance has primarily been studied at the interspecific level, meaning that in most cases we lack a mechanistic understanding of how evolutionarily relevant variation among individuals affects organismal performance. Therefore, functional morphologists need methods that will allow for the analysis of fine-grained intraspecific variation in order to close the path from genes to fitness. We suggest three methodological areas that we believe are well suited for this research program and provide examples of how each can be applied within fish model systems to build our understanding of microevolutionary processes. Specifically, we believe that structural equation modeling, biological robotics, and simultaneous multi-modal functional data acquisition will open up fruitful collaborations among biomechanists, evolutionary biologists, and field biologists. It is only through the combined efforts of all three fields that we will understand the connection between evolution (acting at the level of genes) and natural selection (acting on fitness).
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Affiliation(s)
- David G Matthews
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Terry R Dial
- Department of Biology and Ecology Center, Utah State University, Moab, UT 84322, USA
- Department of Environment and Society, Utah State University, Moab, UT 84322, USA
| | - George V Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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9
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Uji K, Ishikawa A, Shin K, Tayasu I, Kitano J. Strontium isotope analysis of otoliths reveals differences in the habitat salinity among three sympatric stickleback species of the genus Pungitius. Ecol Evol 2023; 13:e10463. [PMID: 37670821 PMCID: PMC10475353 DOI: 10.1002/ece3.10463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
The analysis of otolith Sr isotope ratios (87Sr/86Sr) is a powerful method to study fish migration in freshwater areas. However, few studies have applied this method to study fish movement in brackish-water environments. Furthermore, despite the fact that habitat differentiation has been shown to drive genetic differentiation and reproductive isolation among stickleback fish, no studies have used the otolith 87Sr/86Sr ratios to analyze habitat differentiation between stickleback ecotypes and species. In this study, we analyzed the otolith 87Sr/86Sr ratios of three sympatric stickleback species of the genus Pungitius in the Shiomi River on Hokkaido Island, Japan: P. tymensis, the brackish-water type of the P. pungitius-P. sinensis complex, and the freshwater type of the P. pungitius-P. sinensis complex. First, we created a mixing equation to depict the relationship between habitat salinity and the 87Sr/86Sr ratios of river water. We found that the otolith 87Sr/86Sr ratios differed significantly among the three species, indicating that the three species utilize habitats with different salinities: P. tymensis and the brackish-water type inhabit freshwater and brackish-water environments, respectively, with the freshwater type using intermediate habitats. In addition, we found that some freshwater individuals moved to habitats with higher salinities as they grew. Our study demonstrates that the analysis of otolith 87Sr/86Sr ratios is a useful method for studying the habitat use of fish in brackish-water environments and habitat differentiation among closely related sympatric and parapatric species.
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Affiliation(s)
- Konomi Uji
- Center for Ecological ResearchKyoto UniversityOtsuJapan
| | - Asano Ishikawa
- Ecological Genetics LaboratoryNational Institute of GeneticsMishimaJapan
- Present address:
Department of Integrated BiosciencesGraduate School of Frontier Sciences, The University of TokyoKashiwaJapan
| | - Ki‐Cheol Shin
- Research Institute for Humanity and NatureKyotoJapan
| | - Ichiro Tayasu
- Research Institute for Humanity and NatureKyotoJapan
| | - Jun Kitano
- Ecological Genetics LaboratoryNational Institute of GeneticsMishimaJapan
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10
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Dean LL, Magalhaes IS, D’Agostino D, Hohenlohe P, MacColl ADC. On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback. Mol Biol Evol 2023; 40:msad191. [PMID: 37652053 PMCID: PMC10490448 DOI: 10.1093/molbev/msad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/24/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Rapid evolution of similar phenotypes in similar environments, giving rise to in situ parallel adaptation, is an important hallmark of ecological speciation. However, what appears to be in situ adaptation can also arise by dispersal of divergent lineages from elsewhere. We test whether two contrasting phenotypes repeatedly evolved in parallel, or have a single origin, in an archetypal example of ecological adaptive radiation: benthic-limnetic three-spined stickleback (Gasterosteus aculeatus) across species pair and solitary lakes in British Columbia. We identify two genomic clusters across freshwater populations, which differ in benthic-limnetic divergent phenotypic traits and separate benthic from limnetic individuals in species pair lakes. Phylogenetic reconstruction and niche evolution modeling both suggest a single evolutionary origin for each of these clusters. We detected strong phylogenetic signal in benthic-limnetic divergent traits, suggesting that they are ancestrally retained. Accounting for ancestral state retention, we identify local adaptation of body armor due to the presence of an intraguild predator, the sculpin (Cottus asper), and environmental effects of lake depth and pH on body size. Taken together, our results imply a predominant role for retention of ancestral characteristics in driving trait distribution, with further selection imposed on some traits by environmental factors.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel Santos Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Department of Life Sciences, School of Health and Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Daniele D’Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
- Water Research Center, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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11
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Neto C, Hancock A. Genetic Architecture of Flowering Time Differs Between Populations With Contrasting Demographic and Selective Histories. Mol Biol Evol 2023; 40:msad185. [PMID: 37603463 PMCID: PMC10461413 DOI: 10.1093/molbev/msad185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Understanding the evolutionary factors that impact the genetic architecture of traits is a central goal of evolutionary genetics. Here, we investigate how quantitative trait variation accumulated over time in populations that colonized a novel environment. We compare the genetic architecture of flowering time in Arabidopsis populations from the drought-prone Cape Verde Islands and their closest outgroup population from North Africa. We find that trait polygenicity is severely reduced in the island populations compared to the continental North African population. Further, trait architectures and reconstructed allelic histories best fit a model of strong directional selection in the islands in accord with a Fisher-Orr adaptive walk. Consistent with this, we find that large-effect variants that disrupt major flowering time genes (FRI and FLC) arose first, followed by smaller effect variants, including ATX2 L125F, which is associated with a 4-day reduction in flowering time. The most recently arising flowering time-associated loci are not known to be directly involved in flowering time, consistent with an omnigenic signature developing as the population approaches its trait optimum. Surprisingly, we find no effect in the natural population of EDI-Cvi-0 (CRY2 V367M), an allele for which an effect was previously validated by introgression into a Eurasian line. Instead, our results suggest the previously observed effect of the EDI-Cvi-0 allele on flowering time likely depends on genetic background, due to an epistatic interaction. Altogether, our results provide an empirical example of the effects demographic history and selection has on trait architecture.
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Affiliation(s)
- Célia Neto
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angela Hancock
- Molecular Basis of Adaptation Research Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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12
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Cutter AD. Speciation and development. Evol Dev 2023; 25:289-327. [PMID: 37545126 DOI: 10.1111/ede.12454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Understanding general principles about the origin of species remains one of the foundational challenges in evolutionary biology. The genomic divergence between groups of individuals can spawn hybrid inviability and hybrid sterility, which presents a tantalizing developmental problem. Divergent developmental programs may yield either conserved or divergent phenotypes relative to ancestral traits, both of which can be responsible for reproductive isolation during the speciation process. The genetic mechanisms of developmental evolution involve cis- and trans-acting gene regulatory change, protein-protein interactions, genetic network structures, dosage, and epigenetic regulation, all of which also have roots in population genetic and molecular evolutionary processes. Toward the goal of demystifying Darwin's "mystery of mysteries," this review integrates microevolutionary concepts of genetic change with principles of organismal development, establishing explicit links between population genetic process and developmental mechanisms in the production of macroevolutionary pattern. This integration aims to establish a more unified view of speciation that binds process and mechanism.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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13
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Fair T, Pollen AA. Genetic architecture of human brain evolution. Curr Opin Neurobiol 2023; 80:102710. [PMID: 37003107 DOI: 10.1016/j.conb.2023.102710] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Comparative studies of hominids have long sought to identify mutational events that shaped the evolution of the human nervous system. However, functional genetic differences are outnumbered by millions of nearly neutral mutations, and the developmental mechanisms underlying human nervous system specializations are difficult to model and incompletely understood. Candidate-gene studies have attempted to map select human-specific genetic differences to neurodevelopmental functions, but it remains unclear how to contextualize the relative effects of genes that are investigated independently. Considering these limitations, we discuss scalable approaches for probing the functional contributions of human-specific genetic differences. We propose that a systems-level view will enable a more quantitative and integrative understanding of the genetic, molecular and cellular underpinnings of human nervous system evolution.
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Affiliation(s)
- Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/@TylerFair_
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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14
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Mack KL, Square TA, Zhao B, Miller CT, Fraser HB. Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks. Mol Biol Evol 2023; 40:7048494. [PMID: 36805962 PMCID: PMC10015619 DOI: 10.1093/molbev/msad034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
Cis-regulatory changes are thought to play a major role in adaptation. Threespine sticklebacks have repeatedly colonized freshwater habitats in the Northern Hemisphere, where they have evolved a suite of phenotypes that distinguish them from marine populations, including changes in physiology, behavior, and morphology. To understand the role of gene regulatory evolution in adaptive divergence, here we investigate cis-regulatory changes in gene expression between marine and freshwater ecotypes through allele-specific expression (ASE) in F1 hybrids. Surveying seven ecologically relevant tissues, including three sampled across two developmental stages, we identified cis-regulatory divergence affecting a third of genes, nearly half of which were tissue-specific. Next, we compared allele-specific expression in dental tissues at two timepoints to characterize cis-regulatory changes during development between marine and freshwater fish. Applying a genome-wide test for selection on cis-regulatory changes, we find evidence for lineage-specific selection on several processes between ecotypes, including the Wnt signaling pathway in dental tissues. Finally, we show that genes with ASE, particularly those that are tissue-specific, are strongly enriched in genomic regions of repeated marine-freshwater divergence, supporting an important role for these cis-regulatory differences in parallel adaptive evolution of sticklebacks to freshwater habitats. Altogether, our results provide insight into the cis-regulatory landscape of divergence between stickleback ecotypes across tissues and during development, and support a fundamental role for tissue-specific cis-regulatory changes in rapid adaptation to new environments.
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Affiliation(s)
- Katya L Mack
- Department of Biology, Stanford University, Stanford, CA
| | - Tyler A Square
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Bin Zhao
- Department of Biology, Stanford University, Stanford, CA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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15
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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16
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Wang Y, Wang Y, Cheng X, Ding Y, Wang C, Merilä J, Guo B. Prevalent Introgression Underlies Convergent Evolution in the Diversification of Pungitius Sticklebacks. Mol Biol Evol 2023; 40:7026025. [PMID: 36738166 PMCID: PMC9949714 DOI: 10.1093/molbev/msad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
New mutations and standing genetic variations contribute significantly to repeated phenotypic evolution in sticklebacks. However, less is known about the role of introgression in this process. We analyzed taxonomically and geographically comprehensive genomic data from Pungitius sticklebacks to decipher the extent of introgression and its consequences for the diversification of this genus. Our results demonstrate that introgression is more prevalent than suggested by earlier studies. Although gene flow was generally bidirectional, it was often asymmetric and left unequal genomic signatures in hybridizing species, which might, at least partly, be due to biased hybridization and/or population size differences. In several cases, introgression of variants from one species to another was accompanied by transitions of pelvic and/or lateral plate structures-important diagnostic traits in Pungitius systematics-and frequently left signatures of adaptation in the core gene regulatory networks of armor trait development. This finding suggests that introgression has been an important source of genetic variation and enabled phenotypic convergence among Pungitius sticklebacks. The results highlight the importance of introgression of genetic variation as a source of adaptive variation underlying key ecological and taxonomic traits. Taken together, our study indicates that introgression-driven convergence likely explains the long-standing challenges in resolving the taxonomy and systematics of this small but phenotypically highly diverse group of fish.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yingnan Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoqi Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yongli Ding
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Chongnv Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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17
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Poore HA, Stuart YE, Rennison DJ, Roesti M, Hendry AP, Bolnick DI, Peichel CL. Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution 2023; 77:110-122. [PMID: 36622692 DOI: 10.1093/evolut/qpac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/22/2022] [Accepted: 11/15/2022] [Indexed: 01/10/2023]
Abstract
Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.
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Affiliation(s)
- Hilary A Poore
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Division of Biological Sciences, University of California at San Diego, La Jolla, CA, United States
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Daniel I Bolnick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States.,Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, United States
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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18
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Strickland K, Räsänen K, Kristjánsson BK, Phillips JS, Einarsson A, Snorradóttir RG, Bartrons M, Jónsson ZO. Genome-phenotype-environment associations identify signatures of selection in a panmictic population of threespine stickleback. Mol Ecol 2023; 32:1708-1725. [PMID: 36627230 DOI: 10.1111/mec.16845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/12/2023]
Abstract
Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here, we integrate whole-genome sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP based heritability of all measured traits was high (h2 = 0.42-0.65), indicating adaptive potential for all traits. Environment-association analyses further identified thousands of loci putatively involved in selection, related to genes linked to, for instance, neuron development and protein phosphorylation. Finally, we found that loci linked to water depth were concurrently associated with pelvic spine length variation - supporting the conclusion that divergence in pelvic spine length occurred in the face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.
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Affiliation(s)
- Kasha Strickland
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | - Katja Räsänen
- Department of Aquatic Ecology, EAWAG and Institute of Integrative Biology, ETH, Zurich, Switzerland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | | | - Joseph S Phillips
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland.,Department of Biology, Creighton University, Omaha, Nebraska, USA
| | | | - Ragna G Snorradóttir
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
| | - Mireia Bartrons
- Aquatic Ecology Group, University of Vic (UVic-UCC), Catalonia, Spain
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19
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Turba R, Richmond JQ, Fitz-Gibbon S, Morselli M, Fisher RN, Swift CC, Ruiz-Campos G, Backlin AR, Dellith C, Jacobs DK. Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach. Mol Ecol 2022; 31:6515-6530. [PMID: 36205603 PMCID: PMC10092051 DOI: 10.1111/mec.16722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.
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Affiliation(s)
- Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | | | - Sorel Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | | | - Camm C Swift
- Emeritus, Section of Fishes, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Gorgonio Ruiz-Campos
- Ichthyological Collection, Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station-Santa Ana Office, Santa Ana, California, USA
| | - Chris Dellith
- U.S. Fish and Wildlife Service, Ventura, California, USA
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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20
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Gray OA, Yoo J, Sobreira DR, Jousma J, Witonsky D, Sakabe NJ, Peng YJ, Prabhakar NR, Fang Y, Nobréga MA, Di Rienzo A. A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans. SCIENCE ADVANCES 2022; 8:eade1942. [PMID: 36417539 PMCID: PMC9683707 DOI: 10.1126/sciadv.ade1942] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
In Tibetans, noncoding alleles in EPAS1-whose protein product hypoxia-inducible factor 2α (HIF-2α) drives the response to hypoxia-carry strong signatures of positive selection; however, their functional mechanism has not been systematically examined. Here, we report that high-altitude alleles disrupt the activity of four EPAS1 enhancers in one or more cell types. We further characterize one enhancer (ENH5) whose activity is both allele specific and hypoxia dependent. Deletion of ENH5 results in down-regulation of EPAS1 and HIF-2α targets in acute hypoxia and in a blunting of the transcriptional response to sustained hypoxia. Deletion of ENH5 in mice results in dysregulation of gene expression across multiple tissues. We propose that pleiotropic adaptive effects of the Tibetan alleles in EPAS1 underlie the strong selective signal at this gene.
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Affiliation(s)
- Olivia A. Gray
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jennifer Yoo
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Débora R. Sobreira
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jordan Jousma
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - David Witonsky
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Noboru J. Sakabe
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Ying-Jie Peng
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Nanduri R. Prabhakar
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Yun Fang
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Marcelo A. Nobréga
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Anna Di Rienzo
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
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21
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Beck EA, Bassham S, Cresko WA. Extreme intraspecific divergence in mitochondrial haplotypes makes the threespine stickleback fish an emerging evolutionary mutant model for mito-nuclear interactions. Front Genet 2022; 13:925786. [PMID: 36159975 PMCID: PMC9499175 DOI: 10.3389/fgene.2022.925786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial DNA is primarily maternally inherited in most animals and evolves about 10 times faster than biparentally inherited nuclear DNA. Mitochondrial dysfunction (mt-dys) arises when interactions between the co-evolving mitochondrial and nuclear genomes are perturbed in essential processes like oxidative phosphorylation (OXPHOS). Over time mt-dys can lead to mitochondrial diseases (mt-diseases), which are surprisingly prevalent and include common diseases such as Alzheimer’s, Parkinson’s, and diabetes. Unfortunately, the strong impact that intraspecific mitochondrial and nuclear genetic variation has on mt-disease complicates its study and the development of effective treatments. Animal models have advanced our understanding of mt-disease but their relevance to human conditions is often limited by their relatively low nuclear genetic diversity. Many traditional laboratory models also typically have a single mitochondrial haplotype (mitotype), in stark contrast to over 5,000 mitotypes in humans worldwide. The threespine stickleback fish has an evolutionary history that has made it a favorable evolutionary mutant model (EMM) for studying mito-nuclear interactions and possibly mt-diseases. EMMs are species with naturally evolved states that mimic maladaptive human diseases. In threespine stickleback, a period of isolation followed by introgression of the mitochondrial genome from a sister species resulted in the maintenance of two distinct mitochondrial haplotypes which continue to segregate within many populations of wild stickleback. The existence of two mitogenomes segregating in numerous genetically diverse populations provides a unique system for exploring complex mito-nuclear dynamics. Here we provide the first complete coding region analysis of the two threespine stickleback mitotypes, whose mitogenomic divergence exceeds that of other mammalian models for mitochondrial disease and even that between ancient and modern humans. We find that divergence is not uniform across the mitogenome, but primarily impacts protein coding genes, and significantly impacts proteins in Complex I of OXPHOS. The full characterization of these highly divergent intraspecific mitotypes provides a foundation for the development of threespine stickleback as an EMM for mito-nuclear interactions.
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Affiliation(s)
- Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, United States
- *Correspondence: Emily A. Beck, ; William A. Cresko,
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22
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Oliva C, Hinz NK, Robinson W, Barrett Thompson AM, Booth J, Crisostomo LM, Zanineli S, Tanner M, Lloyd E, O'Gorman M, McDole B, Paz A, Kozol R, Brown EB, Kowalko JE, Fily Y, Duboue ER, Keene AC. Characterizing the genetic basis of trait evolution in the Mexican cavefish. Evol Dev 2022; 24:131-144. [PMID: 35924750 PMCID: PMC9786752 DOI: 10.1111/ede.12412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation. The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabit the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism, and enhanced mechanosensory function. The interfertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex, and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of the measured behavioral and morphological traits. Taken together, this approach provides a novel system to identify genetic underpinnings of naturally occurring variation in morphological and behavioral traits.
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Affiliation(s)
- Camila Oliva
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Wayne Robinson
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Julianna Booth
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | | | - Maureen Tanner
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | - Evan Lloyd
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Morgan O'Gorman
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Brittnee McDole
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alexandra Paz
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Rob Kozol
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Elizabeth B. Brown
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Johanna E. Kowalko
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Yaouen Fily
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Erik R. Duboue
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alex C. Keene
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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23
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Whiting JR, Paris JR, van der Zee MJ, Fraser BA. AF‐vapeR
: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James R. Whiting
- Department of Biosciences University of Exeter Exeter UK
- Department of Biological Sciences University of Calgary Calgary Alberta Canada
| | - Josephine R. Paris
- Department of Biosciences University of Exeter Exeter UK
- Department of Health, Life and Environmental Sciences University of L'Aquila L'Aquila Italy
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24
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Westram AM, Faria R, Johannesson K, Butlin R, Barton N. Inversions and parallel evolution. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210203. [PMID: 35694747 PMCID: PMC9189493 DOI: 10.1098/rstb.2021.0203] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Anja M Westram
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Roger Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nick Barton
- ISTA (Institute of Science and Technology Austria), Klosterneuburg, Austria
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25
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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26
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Roesti M, Gilbert KJ, Samuk K. Chromosomal inversions can limit adaptation to new environments. Mol Ecol 2022; 31:4435-4439. [PMID: 35810344 DOI: 10.1111/mec.16609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason and use simulations to illustrate that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may contribute to the maintenance of polymorphism within species.
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Affiliation(s)
- Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | - Kieran Samuk
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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27
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Morgan C, Knight E, Bomblies K. The meiotic cohesin subunit REC8 contributes to multigenic adaptive evolution of autopolyploid meiosis in Arabidopsis arenosa. PLoS Genet 2022; 18:e1010304. [PMID: 35830475 PMCID: PMC9312919 DOI: 10.1371/journal.pgen.1010304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/25/2022] [Accepted: 06/22/2022] [Indexed: 11/18/2022] Open
Abstract
Genome duplication, which leads to polyploidy, poses challenges to the meiotic segregation of the now-multiple homologous chromosome copies. Genome scan data showed previously that adaptation to polyploid meiosis in autotetraploid Arabidopsis arenosa is likely multigenic, involving genes encoding interacting proteins. But what does this really mean? Functional follow-up studies to genome scans for multigenic traits remain rare in most systems, and thus many mysteries remain about the "functional architecture" of polygenic adaptations. Do different genes all contribute subtle and additive progression towards a fitness optimum, or are there more complex interactions? We previously showed that derived alleles of genes encoding two interacting meiotic axis proteins (ASY1 and ASY3) have additive functional consequences for meiotic adaptation. Here we study derived versus ancestral alleles of the meiotic cohesin subunit REC8, which has roles in chromatin condensation, recruiting the axes, and other critical functions in meiosis. We use genetic and cytological approaches to assess the functional effects of REC8 diploid versus tetraploid alleles, as well as their interaction with ancestral versus derived alleles of ASY1 and ASY3. We show that homozygotes for derived (tetraploid) REC8 alleles have significantly fewer unpaired univalents, a common problem in neotetraploids. Interactions with ASY1 and ASY3 are complex, with the genes in some cases affecting distinct traits, and additive or even antagonistic effects on others. These findings suggest that the road to meiotic adaptation in A. arenosa was perhaps neither straight nor smooth.
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Affiliation(s)
| | | | - Kirsten Bomblies
- Plant Evolutionary Genetics, Institute of Plant Molecular Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
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28
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Kennedy SR, Ying Lim J, Ashley Adams S, Krehenwinkel H, Gillespie RG. What is adaptive radiation? Many manifestations of the phenomenon in an iconic lineage of Hawaiian spiders. Mol Phylogenet Evol 2022; 175:107564. [PMID: 35787456 DOI: 10.1016/j.ympev.2022.107564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022]
Abstract
Adaptive radiation provides the ideal context for identifying and testing the processes that drive evolutionary diversification. However, different adaptive radiations show a variety of different patterns, making it difficult to come up with universal rules that characterize all such systems. Diversification may occur via several mechanisms including non-adaptive divergence, adaptation to novel environments, or character displacement driven by competition. Here, we characterize the ways these different drivers contribute to present-day diversity patterns, using the exemplary adaptive radiation of Hawaiian long-jawed orbweaver (Tetragnatha) spiders. We present the most taxonomically comprehensive phylogenetic hypothesis to date for this group, using 10 molecular markers and representatives from every known species across the archipelago. Among the lineages that make up this remarkable radiation, we find evidence for multiple diversification modalities. Several clades appear to have diversified in allopatry under a narrow range of ecological conditions, highlighting the role of niche conservatism in speciation. Others have shifted into new environments and evolved traits that appear to be adaptive in those environments. Still others show evidence for character displacement by close relatives, often resulting in convergent evolution of stereotyped ecomorphs. All of the above mechanisms seem to have played a role in giving rise to the exceptional diversity of morphological, ecological and behavioral traits represented among the many species of Hawaiian Tetragnatha. Taking all these processes into account, and testing how they operate in different systems, may allow us to identify universal principles underlying adaptive radiation.
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Affiliation(s)
| | - Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Seira Ashley Adams
- Department of Environmental Science, Policy and Management, University of California Berkeley, USA
| | | | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California Berkeley, USA
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29
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Aguirre WE, Reid K, Rivera J, Heins DC, Veeramah KR, Bell MA. Freshwater Colonization, Adaptation, and Genomic Divergence in Threespine Stickleback. Integr Comp Biol 2022; 62:388-405. [PMID: 35660873 PMCID: PMC9405723 DOI: 10.1093/icb/icac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
The Threespine Stickleback is ancestrally a marine fish, but many marine populations breed in fresh water (i.e., are anadromous), facilitating their colonization of isolated freshwater habitats a few years after they form. Repeated adaptation to fresh water during at least 10 My and continuing today has led to Threespine Stickleback becoming a premier system to study rapid adaptation. Anadromous and freshwater stickleback breed in sympatry and may hybridize, resulting in introgression of freshwater-adaptive alleles into anadromous populations, where they are maintained at low frequencies as ancient standing genetic variation. Anadromous stickleback have accumulated hundreds of freshwater-adaptive alleles that are disbursed as few loci per marine individual and provide the basis for adaptation when they colonize fresh water. Recent whole-lake experiments in lakes around Cook Inlet, Alaska have revealed how astonishingly rapid and repeatable this process is, with the frequency of 40% of the identified freshwater-adaptive alleles increasing from negligible (∼1%) in the marine founder to ≥50% within ten generations in fresh water, and freshwater phenotypes evolving accordingly. These high rates of genomic and phenotypic evolution imply very intense directional selection on phenotypes of heterozygotes. Sexual recombination rapidly assembles freshwater-adaptive alleles that originated in different founders into multilocus freshwater haplotypes, and regions important for adaptation to freshwater have suppressed recombination that keeps advantageous alleles linked within large haploblocks. These large haploblocks are also older and appear to have accumulated linked advantageous mutations. The contemporary evolution of Threespine Stickleback has provided broadly applicable insights into the mechanisms that facilitate rapid adaptation.
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Affiliation(s)
- Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614, USA
| | - Kerry Reid
- School of Biological Sciences, Area of Ecology and Biodiversity, University of Hong Kong, Hong Kong, SAR, China.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jessica Rivera
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans 70118, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720, USA
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30
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Genomic changes underlying repeated niche shifts in an adaptive radiation. Evolution 2022; 76:1301-1319. [PMID: 35398888 PMCID: PMC9320971 DOI: 10.1111/evo.14490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 01/21/2023]
Abstract
In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, that is, the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by resequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment, and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.
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Affiliation(s)
- David A. Marques
- Department of BiologyUniversity of VictoriaVictoriaBCV8W 3N5Canada,Aquatic Ecology and Evolution, Institute of Ecology and EvolutionUniversity of BernBernCH‐3012Switzerland,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (EAWAG), Eawag ‐ Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumCH‐6047Switzerland,Natural History Museum BaselBaselCH‐4051Switzerland
| | - Felicity C. Jones
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA,Friedrich Miescher Laboratory of the Max Planck SocietyTübingen72076Germany
| | - Federica Di Palma
- Earlham InstituteNorwichNR4 7UZUnited Kingdom,Department of Biological SciencesUniversity of East AngliaNorwichNR4 7TJUnited Kingdom
| | - David M. Kingsley
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordCalifornia94305USA,Department of Developmental BiologyStanford University School of MedicineStanfordCalifornia94305USA
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31
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Li Q, Lindtke D, Rodríguez-Ramírez C, Kakioka R, Takahashi H, Toyoda A, Kitano J, Ehrlich RL, Chang Mell J, Yeaman S. Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback. Genome Biol Evol 2022; 14:6589818. [PMID: 35594844 PMCID: PMC9178229 DOI: 10.1093/gbe/evac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022] Open
Abstract
Theory predicts that local adaptation should favor the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine versus freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harboring multiple quantitative trait loci for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and lineage-specific genes (LSGs) were enriched around genomic islands, and that all three chromosomes harboring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9× and 2.9× more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
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Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Dorothea Lindtke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Carlos Rodríguez-Ramírez
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa 903-0213, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Rachel L Ehrlich
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
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32
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Kitano J, Ishikawa A, Ravinet M, Courtier-Orgogozo V. Genetic basis of speciation and adaptation: from loci to causative mutations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200503. [PMID: 35634921 PMCID: PMC9149796 DOI: 10.1098/rstb.2020.0503] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will respond to changing environments in the future. Understanding the genetic basis of phenotypic diversification and speciation in natural populations is key to properly answering these questions. The leap forward in genome sequencing technologies has made it increasingly easier to not only investigate the genetic architecture but also identify the variant sites underlying adaptation and speciation in natural populations. Furthermore, recent advances in genome editing technologies are making it possible to investigate the functions of each candidate gene in organisms from natural populations. In this article, we discuss how these recent technological advances enable the analysis of causative genes and mutations and how such analysis can help answer long-standing evolutionary biology questions. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Laboratory of Molecular Ecological Genetics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Chiba 277-8562, Japan
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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33
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Rennison DJ, Peichel CL. Pleiotropy facilitates parallel adaptation in sticklebacks. Mol Ecol 2022; 31:1476-1486. [PMID: 34997980 PMCID: PMC9306781 DOI: 10.1111/mec.16335] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
Highly pleiotropic genes are predicted to be used less often during adaptation, as mutations in these loci are more likely to have negative fitness consequences. Following this logic, we tested whether pleiotropy impacts the probability that a locus will be used repeatedly in adaptation. We used two proxies to estimate pleiotropy: number of phenotypic traits affected by a given genomic region and gene connectivity. We first surveyed 16 independent stream‐lake and three independent benthic‐limnetic ecotype pairs of threespine stickleback to estimate genome‐wide patterns in parallel genomic differentiation. Our analysis revealed parallel divergence across the genome; 30%–37% of outlier regions were shared between at least two independent pairs in either the stream‐lake or benthic‐limnetic comparisons. We then tested whether parallel genomic regions are less pleiotropic than nonparallel regions. Counter to our a priori prediction, parallel genomic regions contained genes with significantly more pleiotropy; that is, influencing a greater number of traits and more highly connected. The increased pleiotropy of parallel regions could not be explained by other genomic factors, as there was no significant difference in mean gene count, mutation or recombination rates between parallel and nonparallel regions. Interestingly, although nonparallel regions contained genes that were less connected and influenced fewer mapped traits on average than parallel regions, they also tended to contain the genes that were predicted to be the most pleiotropic. Taken together, our findings are consistent with the idea that pleiotropy only becomes constraining at high levels and that low or intermediate levels of pleiotropy may be beneficial for adaptation.
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Affiliation(s)
- Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
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34
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Yeaman S. Evolution of polygenic traits under global vs local adaptation. Genetics 2022; 220:6497714. [PMID: 35134196 PMCID: PMC8733419 DOI: 10.1093/genetics/iyab134] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
Observations about the number, frequency, effect size, and genomic distribution of alleles associated with complex traits must be interpreted in light of evolutionary process. These characteristics, which constitute a trait’s genetic architecture, can dramatically affect evolutionary outcomes in applications from agriculture to medicine, and can provide a window into how evolution works. Here, I review theoretical predictions about the evolution of genetic architecture under spatially homogeneous, global adaptation as compared with spatially heterogeneous, local adaptation. Due to the tension between divergent selection and migration, local adaptation can favor “concentrated” genetic architectures that are enriched for alleles of larger effect, clustered in a smaller number of genomic regions, relative to expectations under global adaptation. However, the evolution of such architectures may be limited by many factors, including the genotypic redundancy of the trait, mutation rate, and temporal variability of environment. I review the circumstances in which predictions differ for global vs local adaptation and discuss where progress can be made in testing hypotheses using data from natural populations and lab experiments. As the field of comparative population genomics expands in scope, differences in architecture among traits and species will provide insights into how evolution works, and such differences must be interpreted in light of which kind of selection has been operating.
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Affiliation(s)
- Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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35
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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36
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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37
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Chebib J, Guillaume F. Pleiotropy or linkage? Their relative contributions to the genetic correlation of quantitative traits and detection by multitrait GWA studies. Genetics 2021; 219:6375447. [PMID: 34849850 PMCID: PMC8664587 DOI: 10.1093/genetics/iyab159] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/05/2021] [Indexed: 11/23/2022] Open
Abstract
Genetic correlations between traits may cause correlated responses to selection. Previous models described the conditions under which genetic correlations are expected to be maintained. Selection, mutation, and migration are all proposed to affect genetic correlations, regardless of whether the underlying genetic architecture consists of pleiotropic or tightly linked loci affecting the traits. Here, we investigate the conditions under which pleiotropy and linkage have different effects on the genetic correlations between traits by explicitly modeling multiple genetic architectures to look at the effects of selection strength, degree of correlational selection, mutation rate, mutational variance, recombination rate, and migration rate. We show that at mutation-selection(-migration) balance, mutation rates differentially affect the equilibrium levels of genetic correlation when architectures are composed of pairs of physically linked loci compared to architectures of pleiotropic loci. Even when there is perfect linkage (no recombination within pairs of linked loci), a lower genetic correlation is maintained than with pleiotropy, with a lower mutation rate leading to a larger decrease. These results imply that the detection of causal loci in multitrait association studies will be affected by the type of underlying architectures, whereby pleiotropic variants are more likely to be underlying multiple detected associations. We also confirm that tighter linkage between nonpleiotropic causal loci maintains higher genetic correlations at the traits and leads to a greater proportion of false positives in association analyses.
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Affiliation(s)
- Jobran Chebib
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland.,Organismal and Evolutionary Biology Research Program, University of Helsinki, 00014 Helsinki, Finland
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38
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McCulloch GA, Guhlin J, Dutoit L, Harrop TWR, Dearden PK, Waters JM. Genomic signatures of parallel alpine adaptation in recently evolved flightless insects. Mol Ecol 2021; 30:6677-6686. [PMID: 34592029 DOI: 10.1111/mec.16204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low-elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome-wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within-stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing-development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.
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Affiliation(s)
| | - Joseph Guhlin
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Thomas W R Harrop
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
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39
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Kern AF, Yang GX, Khosla NM, Ang RML, Snyder MP, Fraser HB. Divergent patterns of selection on metabolite levels and gene expression. BMC Ecol Evol 2021; 21:185. [PMID: 34587900 PMCID: PMC8482673 DOI: 10.1186/s12862-021-01915-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022] Open
Abstract
Background Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis—an essential pathway targeted by many antifungal drugs—in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross. Results Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation. Conclusions These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01915-5.
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Affiliation(s)
| | | | - Neil M Khosla
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Roy Moh Lik Ang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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40
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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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41
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Roberts Kingman GA, Lee D, Jones FC, Desmet D, Bell MA, Kingsley DM. Longer or shorter spines: Reciprocal trait evolution in stickleback via triallelic regulatory changes in Stanniocalcin2a. Proc Natl Acad Sci U S A 2021; 118:e2100694118. [PMID: 34321354 PMCID: PMC8346906 DOI: 10.1073/pnas.2100694118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Vertebrates have repeatedly modified skeletal structures to adapt to their environments. The threespine stickleback is an excellent system for studying skeletal modifications, as different wild populations have either increased or decreased the lengths of their prominent dorsal and pelvic spines in different freshwater environments. Here we identify a regulatory locus that has a major morphological effect on the length of stickleback dorsal and pelvic spines, which we term Maser (major spine enhancer). Maser maps in a closely linked supergene complex that controls multiple armor, feeding, and behavioral traits on chromosome IV. Natural alleles in Maser are differentiated between marine and freshwater sticklebacks; however, alleles found among freshwater populations are also differentiated, with distinct alleles found in short- and long-spined freshwater populations. The distinct freshwater alleles either increase or decrease expression of the bone growth inhibitor gene Stanniocalcin2a in developing spines, providing a simple genetic mechanism for either increasing or decreasing spine lengths in natural populations. Genomic surveys suggest many recurrently differentiated loci in sticklebacks are similarly specialized into three or more distinct alleles, providing multiple ancient standing variants in particular genes that may contribute to a range of phenotypes in different environments.
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Affiliation(s)
| | - David Lee
- Stanford University School of Humanities and Sciences, Stanford University, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Danielle Desmet
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- HHMI, Stanford University School of Medicine, Stanford, CA 94305
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42
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Fruciano C, Franchini P, Jones JC. Capturing the rapidly evolving study of adaptation. J Evol Biol 2021; 34:856-865. [PMID: 34145685 DOI: 10.1111/jeb.13871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Research on the genomics of adaptation is rapidly changing. In the last few decades, progress in this area has been driven by methodological advances, not only in the way increasingly large amounts of molecular data are generated (e.g. with high-throughput sequencing), but also in the way these data are analysed. This includes a growing appreciation and quantitative treatment of covariation among units within the same data type (e.g. genes) or across data types (e.g. genes and phenotypes). The development and adoption of more and more integrative tools have resulted in richer and more interesting empirical work. This special issue - comprising methodological, empirical, and review papers - aims to capture a 'snapshot' of this rapidly evolving field. We discuss in particular three important themes in the study of adaptation: the genetic architecture of adaptive variation, protein-coding and regulatory changes, and parallel evolution. We highlight how more traditional key themes in the study of genetic architecture (e.g. the number of loci underlying adaptive traits and the distribution of their effects) are now being complemented by other factors (e.g. how patterns of linkage and number of loci interact to affect the ability to adapt). Similarly, apart from addressing the relative importance of protein-coding and regulatory changes, we now have the tools to look in-depth at specific types of regulatory variation to gain a clearer picture of regulatory networks. Finally, parallel evolution has always been central to the study of adaptation, but now we are often able to address the question of whether - and to what extent - parallelism at the organismal or phenotypic level is matched by parallelism at the genetic level. Perhaps most importantly, we can now determine what mechanisms are driving parallelism (or lack thereof) across levels of biological organization. All these recent methodological developments open up new directions for future studies of adaptive changes across traits, levels of biological organization, demographic contexts and time scales.
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Affiliation(s)
- Carmelo Fruciano
- National Research Council - Institute of Marine Biological Resources and Biotechnologies, Messina, Italy.,Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, PSL Université Paris, Paris, France.,School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Julia C Jones
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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43
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. SCIENCE ADVANCES 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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44
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Jackson HJ, Larsson J, Davison A. Quantitative measures and 3D shell models reveal interactions between bands and their position on growing snail shells. Ecol Evol 2021; 11:6634-6648. [PMID: 34141246 PMCID: PMC8207382 DOI: 10.1002/ece3.7517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 11/10/2022] Open
Abstract
The nature of shell growth in gastropods is useful because it preserves the ontogeny of shape, colour, and banding patterns, making them an ideal system for understanding how inherited variation develops, is established and maintained within a population. However, qualitative scoring of inherited shell characters means there is a lack of knowledge regarding the mechanisms that control fine variation. Here, we combine empirical measures of quantitative variation and 3D modeling of shells to understand how bands are placed and interact. By comparing five-banded Cepaea individuals to shells lacking individual bands, we show that individual band absence has minor but significant impacts upon the position of remaining bands, implying that the locus controlling band presence/absence mainly acts after position is established. Then, we show that the shell grows at a similar rate, except for the region below the lowermost band. This demonstrates that wider bands of Cepaea are not an artifact of greater shell growth on the lower shell; they begin wider and grow at the same rate as other bands. Finally, we show that 3D models of shell shape and banding pattern, inferred from 2D photos using ShellShaper software, are congruent with empirical measures. This work therefore establishes a method that may be used for comparative studies of quantitative banding variation in snail shells, extraction of growth parameters, and morphometrics. In the future, studies that link the banding phenotype to the network of shell matrix proteins involved in biomineralization and patterning may ultimately aid in understanding the diversity of shell forms found in molluscs.
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Affiliation(s)
| | - Jenny Larsson
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Angus Davison
- School of Life SciencesUniversity of NottinghamNottinghamUK
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45
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Abstract
AbstractUnderstanding the genetic architecture of complex trait adaptation in natural populations requires the continued development of tractable models that explicitly confront organismal and environmental complexity. A decade of high-throughput sequencing-based investigations into the genomic basis of migration points to an integrative framework that incorporates quantitative genetics, evolutionary developmental biology, phenotypic plasticity, and epigenetics to explain migration evolution. In this perspective, I argue that the transcontinental migration of the monarch butterfly (Danaus plexippus) can serve as a compelling system to study the mechanism of evolutionary lability of a complex trait. Monarchs show significant phenotypic and genotypic diversity across their global range, with phenotypic switching that allows for explicit study of evolutionary lability. A developmental approach for elucidating how migratory traits are generated and functionally integrated will be important for understanding the evolution of monarch migration traits. I propose a plasticity threshold model to describe migration lability, and I describe novel functional techniques that will help resolve open questions and model assumptions. I conclude by considering the relationships between adaptive genetic architecture, anthropogenic climate change, and conservation management practice and the timeliness of the monarch migration model to illuminate these connections given the rapid decline of the North American migration.
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46
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Paccard A, Hanson D, Stuart YE, von Hippel FA, Kalbe M, Klepaker T, Skúlason S, Kristjánsson BK, Bolnick DI, Hendry AP, Barrett RDH. Repeatability of Adaptive Radiation Depends on Spatial Scale: Regional Versus Global Replicates of Stickleback in Lake Versus Stream Habitats. J Hered 2021; 111:43-56. [PMID: 31690947 DOI: 10.1093/jhered/esz056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The repeatability of adaptive radiation is expected to be scale-dependent, with determinism decreasing as greater spatial separation among "replicates" leads to their increased genetic and ecological independence. Threespine stickleback (Gasterosteus aculeatus) provide an opportunity to test whether this expectation holds for the early stages of adaptive radiation-their diversification in freshwater ecosystems has been replicated many times. To better understand the repeatability of that adaptive radiation, we examined the influence of geographic scale on levels of parallel evolution by quantifying phenotypic and genetic divergence between lake and stream stickleback pairs sampled at regional (Vancouver Island) and global (North America and Europe) scales. We measured phenotypes known to show lake-stream divergence and used reduced representation genome-wide sequencing to estimate genetic divergence. We assessed the scale dependence of parallel evolution by comparing effect sizes from multivariate models and also the direction and magnitude of lake-stream divergence vectors. At the phenotypic level, parallelism was greater at the regional than the global scale. At the genetic level, putative selected loci showed greater lake-stream parallelism at the regional than the global scale. Generally, the level of parallel evolution was low at both scales, except for some key univariate traits. Divergence vectors were often orthogonal, highlighting possible ecological and genetic constraints on parallel evolution at both scales. Overall, our results confirm that the repeatability of adaptive radiation decreases at increasing spatial scales. We suggest that greater environmental heterogeneity at larger scales imposes different selection regimes, thus generating lower repeatability of adaptive radiation at larger spatial scales.
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Affiliation(s)
- Antoine Paccard
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Dieta Hanson
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Yoel E Stuart
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Frank A von Hippel
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
| | - Martin Kalbe
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tom Klepaker
- University of Bergen, Department of Biology, Bergen, Norway
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University College, Sauðárkrókur, Iceland
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, Canada
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47
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Kirch M, Romundset A, Gilbert MTP, Jones FC, Foote AD. Ancient and modern stickleback genomes reveal the demographic constraints on adaptation. Curr Biol 2021; 31:2027-2036.e8. [PMID: 33705715 DOI: 10.1016/j.cub.2021.02.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/05/2021] [Accepted: 02/12/2021] [Indexed: 10/21/2022]
Abstract
Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.1 To address this, we applied a paleogenomics approach2 to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes3 and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.4 The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.
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Affiliation(s)
- Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5A, DK-1353 Copenhagen, Denmark; Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Andrew D Foote
- Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, 7491 Trondheim, Norway; Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, UK.
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48
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Hu J, Wuitchik SJS, Barry TN, Jamniczky HA, Rogers SM, Barrett RDH. Heritability of DNA methylation in threespine stickleback (Gasterosteus aculeatus). Genetics 2021; 217:1-15. [PMID: 33683369 PMCID: PMC8045681 DOI: 10.1093/genetics/iyab001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlying phenotypic change are hypothesized to contribute to population persistence and adaptation in the face of environmental change. To date, few studies have explored the heritability of intergenerationally stable methylation levels in natural populations, and little is known about the relative contribution of cis- and trans-regulatory changes to methylation variation. Here, we explore the heritability of DNA methylation, and conduct methylation quantitative trait loci (meQTLs) analysis to investigate the genetic architecture underlying methylation variation between marine and freshwater ecotypes of threespine stickleback (Gasterosteus aculeatus). We quantitatively measured genome-wide DNA methylation in fin tissue using reduced representation bisulfite sequencing of F1 and F2 crosses, and their marine and freshwater source populations. We identified cytosines (CpG sites) that exhibited stable methylation levels across generations. We found that additive genetic variance explained an average of 24-35% of the methylation variance, with a number of CpG sites possibly autonomous from genetic control. We also detected both cis- and trans-meQTLs, with only trans-meQTLs overlapping with previously identified genomic regions of high differentiation between marine and freshwater ecotypes. Finally, we identified the genetic architecture underlying two key CpG sites that were differentially methylated between ecotypes. These findings demonstrate a potential role for DNA methylation in facilitating adaptation to divergent environments and improve our understanding of the heritable basis of population epigenomic variation.
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Affiliation(s)
- Juntao Hu
- National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Institute of Biodiversity Science, Fudan University, Shanghai 200438, China
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
| | - Sara J S Wuitchik
- Informatics Group, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, Boston University, Boston, MA 02215, USA
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tegan N Barry
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Heather A Jamniczky
- Department of Cell Biology and Anatomy, McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rowan D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC H3A 0C4, Canada
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49
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Kemppainen P, Li Z, Rastas P, Löytynoja A, Fang B, Yang J, Guo B, Shikano T, Merilä J. Genetic population structure constrains local adaptation in sticklebacks. Mol Ecol 2021; 30:1946-1961. [PMID: 33464655 DOI: 10.1111/mec.15808] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/19/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022]
Abstract
Repeated and independent adaptation to specific environmental conditions from standing genetic variation is common. However, if genetic variation is limited, the evolution of similar locally adapted traits may be restricted to genetically different and potentially less optimal solutions or prevented from happening altogether. Using a quantitative trait locus (QTL) mapping approach, we identified the genomic regions responsible for the repeated pelvic reduction (PR) in three crosses between nine-spined stickleback populations expressing full and reduced pelvic structures. In one cross, PR mapped to linkage group 7 (LG7) containing the gene Pitx1, known to control pelvic reduction also in the three-spined stickleback. In the two other crosses, PR was polygenic and attributed to 10 novel QTL, of which 90% were unique to specific crosses. When screening the genomes from 27 different populations for deletions in the Pitx1 regulatory element, these were only found in the population in which PR mapped to LG7, even though the morphological data indicated large-effect QTL for PR in several other populations as well. Consistent with the available theory and simulations parameterized on empirical data, we hypothesize that the observed variability in genetic architecture of PR is due to heterogeneity in the spatial distribution of standing genetic variation caused by >2× stronger population structuring among freshwater populations and >10× stronger genetic isolation by distance in the sea in nine-spined sticklebacks as compared to three-spined sticklebacks.
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Affiliation(s)
- Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Pasi Rastas
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jing Yang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Chinese Sturgeon Research Institute, Three Gorges Corporation, Yichang, China
| | - Baocheng Guo
- The Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takahito Shikano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, The University of Hong Kong, Pokfulam, Hong Kong, SAR
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Magalhaes IS, Whiting JR, D'Agostino D, Hohenlohe PA, Mahmud M, Bell MA, Skúlason S, MacColl ADC. Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations. Nat Ecol Evol 2021; 5:251-261. [PMID: 33257817 PMCID: PMC7858233 DOI: 10.1038/s41559-020-01341-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 10/05/2020] [Indexed: 12/22/2022]
Abstract
Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.
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Affiliation(s)
- Isabel S Magalhaes
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Department of Life Sciences, Whitelands College, University of Roehampton, London, UK.
| | - James R Whiting
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, London, UK.
| | - Daniele D'Agostino
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Muayad Mahmud
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
- Erbil Polytechnic University, Kurdistan Region, Iraq
| | - Michael A Bell
- Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Sauðárkrókur, Iceland
- Icelandic Museum of Natural History, Suðurlandsbraut, Reykjavík, Iceland
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
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